A new approach to single molecule DNA sequencing is proposed. Single molecule methods can be applied to DNA isolated directly from a subject organism, eliminating the need to clone, map and sort DNA fragments prior to sequencing. The need for electrophoretic separation is eliminated and reagent consumption is minimal, promising unprecedented low cost. Single molecule detection has been developed and practiced by physicists and chemists for over 10 years. The crucial optical and detection systems needed for single molecule sequencing now exist. In the Phase I proposal, enzymes and novel labeled nucleotides were identified for use in single molecule sequencing. In Phase II, a nanofabricated flowcell and associated single molecule optics will be developed for monitoring nucleotide incorporation by polymerase. The success of this project will create a new paradigm in DNA sequencing technology. PROPOSED COMMERCIAL APPLICATIONS: A genomic DNA sequencing technology that eliminates the need for cloning, physical mapping and electrophoresis would have great appeal to the academic and industrial genomic research community.